Is it possible to combine a Meta-rig armature with a manually made armature?
While I'm not sure of any limits, I do believe there is a need to have correct bone names and parenting or chain lengths in place for the rig generation to work properly.

The next release of blender (2.79) which is expected to get a beta release soon has some new rigify rigs available with the updated addon version. These include basic human and quadruped rigs as well as bird, cat, horse, shark and wolf.

You can download an early 2.79 test build from here that includes the rigify update, I haven't tried it but I expect the updated rigify addon should work with the current release of blender if you want to copy it across to your current install.